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Modificaomics:deciphering the functions of biomolecule modifications

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Science China Chemistry 2018年第5期61卷 381-392页

作者： Ting Liu Cheng-Jie Ma Bi-Feng Yuan Yu-Qi Feng Key Laboratory of Analytical Chemistry for Biology and Medicine(Ministry of Education) Department of ChemistryWuhan University

The spatiotemporal expression of genes is sophisticatedly controlled through three main layers: transcriptional, translational and post-translational. Now increasing chemical modifications are discovered on genomic DNA, RNA and proteins. These modifications are recognized as additional layer of regulatory mechanisms in controlling gene expression that defines cell status. So far,more than 150 chemical modifications are identified in nucleic acids,and more than 400 discrete types of modifications are identified in proteins. How these modifications are interpreted are fundamental questions to our understanding of living organisms. The omics sciences of systems biology, including genomics, transcriptomics, proteomics, and metabolomics, have been in existence for decades. Due to the large numbers of modifications occurring in DNA, RNA and proteins with regulatory roles, we propose the modificaomics from the words of modification and omics. Modificaomics mainly refers to the comprehensive study of the modifications on DNA, RNA and proteins. In this review, we conceive modificaomics by introducing the discovered modifications in DNA, RNA and proteins as well as summarizing their biological functions. We hope the proposed modificaomics can provide a whole picture of modifications of these biopolymers and simulate the study of the functions of the modifications on DNA, RNA and proteins.

关键词： modificaomies DNA modifications RNA modifications protein modifications functions

Functional Proteomics Driven by Chemical and Computational Approaches

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Chinese Journal of Chemistry 2022年第5期40卷 628-634页

作者： Ying Chen Wei Qin Chu Wang College of Chemistry and Molecular Engineering Peking UniversityBeijing100871 China Peking-Tsinghua Center for Life Science Peking UniversityBeijing100871 China Beijing National Laboratory for Molecular Sciences Peking UniversityBeijing100871 China Synthetic and Functional Biomolecules Center Peking UniversityBeijing100871 China Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking UniversityBeijing100871 China

Functional proteomics is a powerful approach to globally investigate protein functions and their biological ***-based protein profiling(ABPP)has been widely applied to explore the activity and ligandability of proteins in complex biological ***,we summarized our efforts in developing chemical probes and chemical proteomic pipelines to identify protein targets of certain post-translational modifications(PTMs),covalent drugs,natural products and cellular ***,computer-aided proteomic strategies were developed to globally identify functional residues including hyper-reactive cysteines,active sites of selenoproteins and proximal anchors for protein activation.

关键词： Activity-based protein profiling Proteomics protein modifications protein design Target deconwolution

Multifunctional Polymer-protein Conjugates Generated by Multicomponent Reactions

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Chinese Journal of Chemistry 2021年第8期39卷 2287-2295页

作者： Tengfei Mao Chongyu Zhu Lei Tao State Key Laboratory of NBC Protection for Civilian Beijing 102205China The Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology(Ministry of Education) Department of ChemistryTsinghua UniversityBeijing 100084China Department of Materials Science Fudan UniversityShanghai 200433China

Recently,multifunctional polymers for protein conjugation have been facilely synthesized through the multicomponent reactions(MCRs).In this mini-review,current progress in the generation of multifuncti onal polymers with protei n-reactive groups via MCRs is *** mult functional polymers react with model therapeutic proteins,forming multifunctional polymer-protein conjugates,which are prototypes of sophisticated theranostic agents and antibacterial vaccine *** comparison with the traditional multi-step synthesis,the preparation of multifunctional polymers for protein conjugation through MCRs is straightforward and *** to these properties,MCRs have the potential to become a new general strategy to achieve polymer-protein conjugates for biological and medical applications.

关键词： protein modifications Conjugation Poly(ethylene glycol)(PEG) Multicomponent reactions Polymers

Colloidal Virus Particles with Hierarchical Nanomorphology and Facile Biosurface Modification

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Chinese Journal of Chemistry 2022年第8期40卷 946-952页

作者： Hailan Zhong Hao Wu Shuoran Chen Liwei Cao Changqing Ye Fan Xia Fengyu Li College of Chemistry and Materials Science Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and ApplicationsGuangdong Engineering&Technology Research Centre of Graphene-like Materials and ProductsJinan UniversityGuangzhouGuangdong 510632China Research Center for Green Printing Nanophotonic Materials Jiangsu Key Laboratory for Environmental Functional MaterialsSuzhou University of Science and TechnologySuzhouJiangsu 215009China School of Materials Science and Engineering Zhengzhou UniversityZhengzhouHenan 450001China Zhejiang Institute China University of GeosciencesHangzhouZhejiang 311305China

Aiming to the enormous requirement for the epidemic defense researches,we designed and constructed a spherical colloidal virus particle(CVP)to mimic nature virus in morphology,physical,chemical and biological characteristics,via coating spiky protein on col-loidal nanoparticles(CNPs)core with bulge hierarchical *** novel virus-like surface nanoparticles can easily be *** physical,chemical nature and the formation mechanism of the prepared CVPs were characterized and *** synthesized CVPs are similar in size and envelope thickness to common natural *** was demonstrated that the diameter of CVPs is about 238±12 nm,including an 8 nm thickness protein crown with bulges of 33 nm in average *** CVPs with an isoelectric point of 4.5,meets the native virus property of negative charge under neutral *** protein crown enhances the roughness remarkably from 10 nm(CNPs)to 22 nm(CVPs)determined by atomic force *** to the biomimetic rough morphology,the CVPs show greatly superior cellular uptake performance compared to CNPs,ovalbumin(OVA)and smoothed col-loidal particles(SCPs).The formation mechanism of protein crown with specific thickness can be attributed to the electrostatic in-teraction,protein's flexible structure and specific *** results indicate that the as-prepared artificial virions mimic na-ture viruses in multi-dimension,in terms of size,surface rough morphology,surface negative charge and glycoprotein envelope *** synthetic colloidal virus particles pave a facile way toward engineering virus particles substitute for virus-related diseases prevention,diagnostics and cellular delivery vectors.

关键词： Nanoparticles protein modifications Biomimetic synthesis Virus particles Cellular delivery

A New Pyridoxal Derivative for Transamination of N-Terminus of proteins

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Chinese Journal of Chemistry 2011年第8期29卷 1715-1720页

作者：张美娟张学梅李娟郭庆祥 Department of Chemistry University of Science and Technology of China Hefei Anhui 230026 China Department of Chemistry Tsinghua University Beijing 100084 China

A new pyridoxal-5-phosphate （PLP） derivative FHMDP was developed for the transamination of different pep- tides with three most hindered amino acid residues （Leu, Ile, Val） as their N-terminus. Compared to the previously reported reactions of PLP derivatives, the N-terminus transamination could be accomplished efficiently with the new compound.

关键词： transamination N-terminus protein bioconjugation PLP derivative peptides protein modifications

Genetically Encoded Residue Selective Photo-Crosslinker to Capture and Identify protein Interactions in Living Cells

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Genetically Encoded Residue Selective Photo-Crosslinker to C...